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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2016-09-21 22:45:24 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2016-09-26 03:21:27 +0200 |
| commit | ad34f0ac96f6f3f074d438b6c19d8211eefc3fa3 (patch) | |
| tree | 44f25ed613932ddd6b772e2327aeb72692db3f57 | |
| parent | 2301fd3e4d3d1789f63e19d9f46146e157d7e610 (diff) | |
| download | patches-ad34f0ac96f6f3f074d438b6c19d8211eefc3fa3.tar patches-ad34f0ac96f6f3f074d438b6c19d8211eefc3fa3.tar.gz | |
gnu: Add r-deseq2.
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f11a89ec45..0787d4bfeb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5125,6 +5125,51 @@ microarrays.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-deseq2 + (package + (name "r-deseq2") + (version "1.12.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq2" version)) + (sha256 + (base32 + "12h77f0dpi5xaj7aqf50kkyn6lq9j7bcsly1r0ffmyfcszrp1sfx")))) + (properties `((upstream-name . "DESeq2"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'link-against-armadillo + (lambda _ + (substitute* "src/Makevars" + (("PKG_LIBS =" prefix) + (string-append prefix "-larmadillo")))))))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "http://bioconductor.org/packages/DESeq2") + (synopsis "Differential gene expression analysis") + (description + "This package provides functions to estimate variance-mean dependence in +count data from high-throughput nucleotide sequencing assays and test for +differential expression based on a model using the negative binomial +distribution.") + (license license:lgpl3+))) + (define-public vsearch (package (name "vsearch") |